S1 nuclease protection

S1 nuclease protection is a method used in transcript analysis to ascertain the start site of transcription.

The procedure is as follows:

1. Design a 5' end-labelled probe to hybridise to a region on DNA spanning the transcription start point - i.e. from within the promoter to within exon 1.
2. Hybridise this probe to the transcript.
3. Digest with S1 nuclease; the hybridised region is protected and the rest is degraded
4. An unknown number of nucleotides (x nts) has been removed from the 3' end of the probe; ascertain x using electrophoresis with 3 lanes:

- Markers
- Probe
- Protected probe

5. The distance on the gel between the probe and the protected probe corresponds to x nts.